PASH Analysis (CPG)
Seraphina Shi
CPGs reads sumary
## 129 observations with both PAH31 and CPG sites data from 104 unique subjects.## cg05575921 cg21566642 cg01940273 cg21161138
## Min. :0.6293 Min. :0.2730 Min. :0.4667 Min. :0.5821
## 1st Qu.:0.8116 1st Qu.:0.3904 1st Qu.:0.5521 1st Qu.:0.6856
## Median :0.8458 Median :0.4258 Median :0.5765 Median :0.7076
## Mean :0.8391 Mean :0.4220 Mean :0.5775 Mean :0.7047
## 3rd Qu.:0.8840 3rd Qu.:0.4603 3rd Qu.:0.6064 3rd Qu.:0.7326
## Max. :0.9173 Max. :0.5670 Max. :0.6906 Max. :0.7780
## cg03329539 cg03636183 cg09935388 cg19859270
## Min. :0.2759 Min. :0.4846 Min. :0.5959 Min. :0.8477
## 1st Qu.:0.3394 1st Qu.:0.6420 1st Qu.:0.7794 1st Qu.:0.9078
## Median :0.3625 Median :0.6730 Median :0.8085 Median :0.9157
## Mean :0.3657 Mean :0.6678 Mean :0.8013 Mean :0.9144
## 3rd Qu.:0.3885 3rd Qu.:0.6950 3rd Qu.:0.8371 3rd Qu.:0.9242
## Max. :0.4879 Max. :0.7495 Max. :0.8825 Max. :0.9406
## cg09198866 cg00811020 cg01411366
## Min. :0.8682 Min. :0.08161 Min. :0.2108
## 1st Qu.:0.8999 1st Qu.:0.14166 1st Qu.:0.3945
## Median :0.9113 Median :0.16929 Median :0.4324
## Mean :0.9115 Mean :0.16888 Mean :0.4303
## 3rd Qu.:0.9221 3rd Qu.:0.19690 3rd Qu.:0.4654
## Max. :0.9528 Max. :0.34424 Max. :0.6284PAH31 ~ CPG site
not adjusted for confounders
adjusted for confounders
current 5mc ~ CPG site
not adjusted for confounders
cummulative 5mc ~ CPG site
not adjusted for confounders
childhood 5mc ~ CPG site
not adjusted for confounders
CPG site ~ Current fuel type
GEE (with confounders, Smokeless ref)
The numbers of observations with each current fuel type:
##
## Smokeles Smoky Wood_and_or_Plant
## 18 100 14In this section, we perform the generalized estimating equations (GEE) to evaluate the associations between current fuel type and each CpG site reads with the formula: \[ \begin{aligned} Y = & \beta_0 + \beta_1 * I(\text{Smoky}) + \beta_2 * I(\text{Wood_and_or_Plant}) \\ & + \beta_3 * county + \beta_4 * BMI + \beta_5 * ses + \beta_6 * edu + \epsilon \end{aligned} \]
Results:
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## The estimated average EAA differences of Smoky fuel type to Smokeless fuel yupes:## coefficient std ci_lower ci_upper p_val sig_level
## cg05575921 -0.0453 0.0103 -0.0655 -0.0252 0.000010 <= 0.001
## cg21566642 -0.0244 0.0148 -0.0535 0.0047 0.100600 > 0.05
## cg01940273 -0.0262 0.0100 -0.0459 -0.0066 0.008778 <= 0.01
## cg21161138 -0.0204 0.0090 -0.0380 -0.0027 0.023707 <= 0.05
## cg03329539 -0.0017 0.0081 -0.0176 0.0141 0.830765 > 0.05
## cg03636183 -0.0456 0.0102 -0.0655 -0.0256 0.000007 <= 0.001
## cg09935388 -0.0039 0.0134 -0.0301 0.0223 0.771875 > 0.05
## cg19859270 -0.0014 0.0049 -0.0110 0.0082 0.772623 > 0.05
## cg09198866 0.0015 0.0051 -0.0084 0.0115 0.762496 > 0.05
## cg00811020 0.0051 0.0096 -0.0138 0.0240 0.598073 > 0.05
## cg01411366 -0.0055 0.0148 -0.0345 0.0235 0.711272 > 0.05## The estimated average EAA differences of Wood and/or Plant fuel type to Smokeless fuel yupes:## coefficient std ci_lower ci_upper p_val sig_level
## cg05575921 -0.0572 0.0134 -0.0835 -0.0309 0.000020 <= 0.001
## cg21566642 -0.0316 0.0204 -0.0716 0.0084 0.121770 > 0.05
## cg01940273 -0.0283 0.0131 -0.0540 -0.0027 0.030076 <= 0.05
## cg21161138 -0.0067 0.0118 -0.0298 0.0163 0.568266 > 0.05
## cg03329539 -0.0060 0.0114 -0.0284 0.0163 0.596737 > 0.05
## cg03636183 -0.0388 0.0125 -0.0633 -0.0144 0.001843 <= 0.01
## cg09935388 -0.0056 0.0128 -0.0308 0.0196 0.662370 > 0.05
## cg19859270 -0.0053 0.0051 -0.0153 0.0048 0.305401 > 0.05
## cg09198866 -0.0029 0.0058 -0.0143 0.0085 0.617203 > 0.05
## cg00811020 -0.0075 0.0152 -0.0373 0.0222 0.620596 > 0.05
## cg01411366 0.0288 0.0210 -0.0124 0.0699 0.170474 > 0.05GEE (without confounders, Smokeless ref)
The numbers of observations with each current fuel type:
##
## Smokeles Smoky Wood_and_or_Plant
## 18 100 14In this section, we perform the generalized estimating equations (GEE) to evaluate the associations between current fuel type and each CpG site reads with the formula: \[ \begin{aligned} Y = & \beta_0 + \beta_1 * I(\text{Smoky}) + \beta_2 * I(\text{Wood_and_or_Plant}) \\ & + \epsilon \end{aligned} \]
Results:
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## [1] "Fitting with 132 observations."
## The estimated average EAA differences of Smoky fuel type to Smokeless fuel yupes:## coefficient std ci_lower ci_upper p_val sig_level
## cg05575921 -0.0421 0.0075 -0.0568 -0.0273 0.000000 <= 0.001
## cg21566642 -0.0108 0.0133 -0.0368 0.0153 0.417026 > 0.05
## cg01940273 -0.0135 0.0097 -0.0326 0.0056 0.166367 > 0.05
## cg21161138 -0.0153 0.0082 -0.0313 0.0006 0.060034 > 0.05
## cg03329539 0.0039 0.0077 -0.0113 0.0190 0.616536 > 0.05
## cg03636183 -0.0340 0.0080 -0.0496 -0.0184 0.000020 <= 0.001
## cg09935388 -0.0052 0.0121 -0.0290 0.0186 0.668365 > 0.05
## cg19859270 -0.0006 0.0049 -0.0102 0.0089 0.895578 > 0.05
## cg09198866 0.0013 0.0048 -0.0081 0.0107 0.784650 > 0.05
## cg00811020 -0.0039 0.0081 -0.0198 0.0119 0.625883 > 0.05
## cg01411366 -0.0026 0.0143 -0.0306 0.0254 0.855045 > 0.05## The estimated average EAA differences of Wood and/or Plant fuel type to Smokeless fuel yupes:## coefficient std ci_lower ci_upper p_val sig_level
## cg05575921 -0.0586 0.0143 -0.0866 -0.0307 0.000040 <= 0.001
## cg21566642 -0.0262 0.0214 -0.0682 0.0159 0.222283 > 0.05
## cg01940273 -0.0221 0.0137 -0.0490 0.0048 0.107285 > 0.05
## cg21161138 -0.0026 0.0112 -0.0245 0.0194 0.818688 > 0.05
## cg03329539 -0.0023 0.0117 -0.0253 0.0208 0.847698 > 0.05
## cg03636183 -0.0339 0.0124 -0.0582 -0.0096 0.006268 <= 0.01
## cg09935388 -0.0047 0.0121 -0.0285 0.0190 0.696191 > 0.05
## cg19859270 -0.0050 0.0055 -0.0158 0.0058 0.363770 > 0.05
## cg09198866 -0.0027 0.0058 -0.0141 0.0086 0.638459 > 0.05
## cg00811020 -0.0117 0.0143 -0.0398 0.0163 0.411798 > 0.05
## cg01411366 0.0264 0.0214 -0.0155 0.0683 0.217460 > 0.05